At the outbreak of the Great Patriotic War, the crew of the vessel was at the Baltic Shipyard, where it had been transferred to from the Northern Fleet for repair. The submariners shared the hardships of the 1941-1942 winter with the besieged Leningraders. The D-2 submarine went on its first combat patrol under command of Captain 3rd rank R.V. Lindenberg, which lasted from September 23 to November 4, 1942. Already the next day after getting underway, it found itself in an antisubmarine net. The commanders undertook full speed ahead with simultaneous main ballast blowing. The ship got surfaced, but it could not get out of the net. For two nights, the emergency team was cutting steel hemps in cold weather in a seaway (during the day the ship was submerged to prevent the enemy from discovering it). The work was supervised by Lieutenant commander S.N. Bogorad (later commander of one of the Baltic Schukas, Hero of the Soviet Union). The D-2 forced its way to the Southern Baltic, torpedoed the vessel Jacubus Friezen at Island Bornholm, and five days later attacked a convoy which consisted of two railway ferries carrying Wehrmacht soldiers. One of these ferries was seriously damaged, more than 600 soldiers and officers perished. The ship was pursued by antisubmarine ships; 48 depth charges were dropped on it within four hours, but the D-2 safely returned to Leningrad where it was met by Commander-in-Chief of the Navy Nikolai Gerasimovich Kuznetsov. And in total, the combat record of the ship counts 12 torpedo attacks, four enemy vessels...
Until 1956, the D-2 was part of the Baltic Fleet. Then it was decommissioned from the Navy and transformed into a damage control training station (UTS-6). At the station, the technique of preventing the influx of water into the tight hull of the submarine was worked out, along with the methods of firefighting, the ways to secure endurance of the machinery, as well as the tasks of shallow diving training. The submarine was used in the Navy in this capacity for the subsequent 31 years until 1987.